Variant report

Variant	rs2276986
Chromosome Location	chr5:1797735-1797736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1796401-1798408	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:1797678-1797973	A549	lung:	n/a	n/a
3	POLR2A	chr5:1797193-1797739	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr5:1794105-1798433	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:1795858-1798914	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:1797470-1798348	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:1795389-1798353	K562	blood:	n/a	n/a
8	POLR2A	chr5:1795148-1798343	K562	blood:	n/a	n/a
9	POLR2A	chr5:1796681-1797972	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:1795095-1798455	GM12891	blood:	n/a	n/a
11	POLR2A	chr5:1796869-1798479	GM12892	blood:	n/a	n/a
12	POLR2A	chr5:1796397-1798482	GM12891	blood:	n/a	n/a
13	POLR2A	chr5:1796440-1797776	HL-60	blood:	n/a	n/a
14	POLR2A	chr5:1794429-1798387	Raji	blood:	n/a	n/a
15	POLR2A	chr5:1795870-1798186	GM19193	blood:	n/a	n/a
16	POLR2A	chr5:1795849-1798500	GM12892	blood:	n/a	n/a
17	POLR2A	chr5:1794420-1798546	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr5:1795310-1797914	HEK293	kidney:	n/a	n/a
19	POLR2A	chr5:1795250-1798842	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:1796025-1798395	NB4	blood:	n/a	n/a
21	POLR2A	chr5:1796311-1798415	GM12892	blood:	n/a	n/a
22	POLR2A	chr5:1795906-1798390	GM12891	blood:	n/a	n/a
23	POLR2A	chr5:1796385-1798404	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr5:1797599-1798566	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:1795385-1798427	K562	blood:	n/a	n/a
26	POLR2A	chr5:1795667-1798330	K562	blood:	n/a	n/a
27	POLR2A	chr5:1796445-1798029	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:1796351-1798264	K562	blood:	n/a	n/a
29	POLR2A	chr5:1796391-1798435	GM12878	blood:	n/a	n/a
30	ZNF263	chr5:1797489-1798348	HEK293-T-REx	kidney:	n/a	chr5:1797586-1797595
31	POLR2A	chr5:1796577-1798322	HepG2	liver:	n/a	n/a
32	POLR2A	chr5:1794860-1798520	K562	blood:	n/a	n/a
33	POLR2A	chr5:1795581-1798300	K562	blood:	n/a	n/a
34	POLR2A	chr5:1795050-1798377	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:1795289-1798422	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr5:1795342-1801944	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr5:1796042-1797928	GM18505	blood:	n/a	n/a
38	POLR2A	chr5:1795433-1798095	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr5:1797592-1798008	K562	blood:	n/a	n/a
40	POLR2A	chr5:1795560-1798480	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr5:1795523-1798583	GM12892	blood:	n/a	n/a
42	POLR2A	chr5:1795584-1798472	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1777867..1779395-chr5:1796687..1799686,2	K562	blood:
2	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
3	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
4	chr5:1769932..1772068-chr5:1795879..1799269,3	MCF-7	breast:
5	chr5:1745339..1747054-chr5:1797446..1799846,2	K562	blood:

No data

Variant related genes	Relation type
NDUFS6	TF binding region
ENSG00000249116	Chromatin interaction
ENSG00000113430	Chromatin interaction
ENSG00000249326	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11133910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11133911	0.96[ASN][1000 genomes]
rs11133912	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13187162	0.94[ASN][1000 genomes]
rs1845288	0.99[ASN][1000 genomes]
rs1873926	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2242412	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34233926	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35380881	0.96[ASN][1000 genomes]
rs3756343	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3756345	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs3756346	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs3776141	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs3776142	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3776143	0.96[ASN][1000 genomes]
rs3776144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776145	0.99[ASN][1000 genomes]
rs3776146	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776149	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3822364	0.96[ASN][1000 genomes]
rs4147769	0.99[ASN][1000 genomes]
rs4147770	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147772	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4147773	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4975731	0.83[GIH][hapmap]
rs4975845	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4975847	0.84[JPT][hapmap]
rs4975848	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4975849	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs4975851	0.95[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs4975852	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4975853	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs55883912	0.97[ASN][1000 genomes]
rs6555012	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6863367	0.96[ASN][1000 genomes]
rs7702843	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs972890	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs972891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs972892	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs974722	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv1033147	chr5:1717303-1815821	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1020703	chr5:1724199-1814288	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv537608	chr5:1724199-1814288	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1790600-1797800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:1791000-1798800	Weak transcription	Fetal Brain Male	brain
3	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:1793200-1798800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:1794000-1798600	Weak transcription	Stomach Mucosa	stomach
6	chr5:1794400-1798200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:1794400-1799200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:1794600-1797800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:1794600-1798200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:1794600-1799200	Weak transcription	Small Intestine	intestine
11	chr5:1794800-1798800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:1795200-1797800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:1795400-1797800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:1795400-1798000	Strong transcription	Fetal Stomach	stomach
15	chr5:1795800-1799000	Strong transcription	Fetal Intestine Small	intestine
16	chr5:1796000-1797800	Strong transcription	Primary T cells from cord blood	blood
17	chr5:1796000-1797800	Strong transcription	Gastric	stomach
18	chr5:1796000-1797800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr5:1796000-1797800	Strong transcription	NHLF	lung
20	chr5:1796000-1798200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:1796000-1798400	Strong transcription	Primary B cells from cord blood	blood
22	chr5:1796000-1798400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:1796000-1798600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr5:1796000-1798600	Strong transcription	Thymus	Thymus
25	chr5:1796000-1798800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:1796000-1798800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:1796000-1798800	Strong transcription	Brain Substantia Nigra	brain
28	chr5:1796000-1799000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:1796200-1797800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:1796200-1797800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:1796200-1797800	Strong transcription	Liver	Liver
32	chr5:1796200-1797800	Genic enhancers	GM12878-XiMat	blood
33	chr5:1796200-1797800	Strong transcription	HMEC	breast
34	chr5:1796200-1798200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:1796200-1798200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:1796200-1798400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:1796200-1798600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:1796200-1798800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:1796200-1798800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:1796200-1798800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr5:1796400-1797800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:1796400-1798000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr5:1796400-1798000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:1796400-1798000	Strong transcription	A549	lung
45	chr5:1796400-1798200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:1796400-1798400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr5:1796400-1798600	Strong transcription	Brain Anterior Caudate	brain
48	chr5:1796400-1798600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr5:1796400-1798800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:1796400-1798800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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